Literature DB >> 16534544

Pulling the chromatin.

C Claudet1, J Bednar.   

Abstract

Nucleosome is the basic subunit of the chromatin, which organizes the genomic DNA within the cell nucleus. It was understood in the last decade that beside the DNA compaction it plays an important role in the regulation of the gene expression. In its intact form, the nucleosome represents an important mechanical barrier and, among others, it prevents access to the DNA and blocks the transcription elongation. Therefore, it has become important to know the forces and energies necessary to destabilize the nucleosome in order to understand the DNA-related processes. Stretching the chromatin fibre using micromanipulation techniques (e.g. optical tweezers) is an ideal approach to study the nucleosomal stability and the parameters that can modify it. In this short review we will discuss the existing data and potential difficulties that this state-of-the-art technique still has to overcome.

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Year:  2006        PMID: 16534544     DOI: 10.1140/epje/i2005-10072-0

Source DB:  PubMed          Journal:  Eur Phys J E Soft Matter        ISSN: 1292-8941            Impact factor:   1.890


  42 in total

1.  Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA.

Authors:  Brent D Brower-Toland; Corey L Smith; Richard C Yeh; John T Lis; Craig L Peterson; Michelle D Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2002-02-19       Impact factor: 11.205

2.  Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers.

Authors:  M L Bennink; S H Leuba; G H Leno; J Zlatanova; B G de Grooth; J Greve
Journal:  Nat Struct Biol       Date:  2001-07

3.  Histone-DNA binding free energy cannot be measured in dilution-driven dissociation experiments.

Authors:  A Thåström; J M Gottesfeld; K Luger; J Widom
Journal:  Biochemistry       Date:  2004-01-27       Impact factor: 3.162

4.  Functional analysis of nucleosome assembly protein, NAP-1. The negatively charged COOH-terminal region is not necessary for the intrinsic assembly activity.

Authors:  T Fujii-Nakata; Y Ishimi; A Okuda; A Kikuchi
Journal:  J Biol Chem       Date:  1992-10-15       Impact factor: 5.157

5.  Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes.

Authors:  Brent Brower-Toland; David A Wacker; Robert M Fulbright; John T Lis; W Lee Kraus; Michelle D Wang
Journal:  J Mol Biol       Date:  2004-12-22       Impact factor: 5.469

6.  Driving proteins off DNA using applied tension.

Authors:  J F Marko; E D Siggia
Journal:  Biophys J       Date:  1997-10       Impact factor: 4.033

7.  Crystal structure of the nucleosome core particle at 2.8 A resolution.

Authors:  K Luger; A W Mäder; R K Richmond; D F Sargent; T J Richmond
Journal:  Nature       Date:  1997-09-18       Impact factor: 49.962

8.  Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation.

Authors:  K J Polach; J Widom
Journal:  J Mol Biol       Date:  1995-11-24       Impact factor: 5.469

9.  Nucleosome core particle stability and conformational change. Effect of temperature, particle and NaCl concentrations, and crosslinking of histone H3 sulfhydryl groups.

Authors:  J Ausio; D Seger; H Eisenberg
Journal:  J Mol Biol       Date:  1984-06-15       Impact factor: 5.469

10.  Nucleosome dissociation at physiological ionic strengths.

Authors:  R W Cotton; B A Hamkalo
Journal:  Nucleic Acids Res       Date:  1981-01-24       Impact factor: 16.971

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  5 in total

Review 1.  Chromatin physics: Replacing multiple, representation-centered descriptions at discrete scales by a continuous, function-dependent self-scaled model.

Authors:  C Lavelle; A Benecke
Journal:  Eur Phys J E Soft Matter       Date:  2006-02-22       Impact factor: 1.890

2.  Homebuilt single-molecule scanning confocal fluorescence microscope studies of single DNA/protein interactions.

Authors:  Haocheng Zheng; Lori S Goldner; Sanford H Leuba
Journal:  Methods       Date:  2007-03       Impact factor: 3.608

3.  Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs.

Authors:  A Benecke
Journal:  Eur Phys J E Soft Matter       Date:  2006-03-07       Impact factor: 1.890

Review 4.  Expedient placement of two fluorescent dyes for investigating dynamic DNA protein interactions in real time.

Authors:  Sanford H Leuba; Syam P Anand; Joel M Harp; Saleem A Khan
Journal:  Chromosome Res       Date:  2008       Impact factor: 5.239

Review 5.  Chromatin fiber dynamics under tension and torsion.

Authors:  Christophe Lavelle; Jean-Marc Victor; Jordanka Zlatanova
Journal:  Int J Mol Sci       Date:  2010-04-12       Impact factor: 5.923

  5 in total

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